PLUMED-NEST by plumed-nest

Project ID: plumID:25.003
Source: Chignolin/OPES/plumed.dat
Originally used with PLUMED version: 2.10
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
Click on the labels of the actions for more information on what each action computes
# vim: ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 


#generated with gmx editconf -f topol.tpr -o reference.pdb, see https://www.plumed.org/doc-v2.7/user-doc/html/_m_o_l_i_n_f_o.html
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-166

# Select Calpha
The WHOLEMOLECULES action with label  calculates somethingPROTEINThe GROUP action with label PROTEIN calculates the following quantities: Quantity    Type    Description  
PROTEIN atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-166
CAThe GROUP action with label CA calculates the following quantities: Quantity    Type    Description  
CA atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=5,26,47,61,73,88,102,109,123,147

d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=26,5
d2The DISTANCE action with label d2 calculates the following quantities: Quantity    Type    Description  
d2 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=47,5
d3The DISTANCE action with label d3 calculates the following quantities: Quantity    Type    Description  
d3 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=47,26
d4The DISTANCE action with label d4 calculates the following quantities: Quantity    Type    Description  
d4 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=61,5
d5The DISTANCE action with label d5 calculates the following quantities: Quantity    Type    Description  
d5 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=61,26
d6The DISTANCE action with label d6 calculates the following quantities: Quantity    Type    Description  
d6 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=61,47
d7The DISTANCE action with label d7 calculates the following quantities: Quantity    Type    Description  
d7 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=73,5
d8The DISTANCE action with label d8 calculates the following quantities: Quantity    Type    Description  
d8 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=73,26
d9The DISTANCE action with label d9 calculates the following quantities: Quantity    Type    Description  
d9 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=73,47
d10The DISTANCE action with label d10 calculates the following quantities: Quantity    Type    Description  
d10 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=73,61
d11The DISTANCE action with label d11 calculates the following quantities: Quantity    Type    Description  
d11 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=88,5
d12The DISTANCE action with label d12 calculates the following quantities: Quantity    Type    Description  
d12 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=88,26
d13The DISTANCE action with label d13 calculates the following quantities: Quantity    Type    Description  
d13 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=88,47
d14The DISTANCE action with label d14 calculates the following quantities: Quantity    Type    Description  
d14 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=88,61
d15The DISTANCE action with label d15 calculates the following quantities: Quantity    Type    Description  
d15 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=88,73
d16The DISTANCE action with label d16 calculates the following quantities: Quantity    Type    Description  
d16 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=102,5
d17The DISTANCE action with label d17 calculates the following quantities: Quantity    Type    Description  
d17 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=102,26
d18The DISTANCE action with label d18 calculates the following quantities: Quantity    Type    Description  
d18 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=102,47
d19The DISTANCE action with label d19 calculates the following quantities: Quantity    Type    Description  
d19 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=102,61
d20The DISTANCE action with label d20 calculates the following quantities: Quantity    Type    Description  
d20 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=102,73
d21The DISTANCE action with label d21 calculates the following quantities: Quantity    Type    Description  
d21 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=102,88
d22The DISTANCE action with label d22 calculates the following quantities: Quantity    Type    Description  
d22 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=109,5
d23The DISTANCE action with label d23 calculates the following quantities: Quantity    Type    Description  
d23 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=109,26
d24The DISTANCE action with label d24 calculates the following quantities: Quantity    Type    Description  
d24 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=109,47
d25The DISTANCE action with label d25 calculates the following quantities: Quantity    Type    Description  
d25 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=109,61
d26The DISTANCE action with label d26 calculates the following quantities: Quantity    Type    Description  
d26 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=109,73
d27The DISTANCE action with label d27 calculates the following quantities: Quantity    Type    Description  
d27 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=109,88
d28The DISTANCE action with label d28 calculates the following quantities: Quantity    Type    Description  
d28 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=109,102
d29The DISTANCE action with label d29 calculates the following quantities: Quantity    Type    Description  
d29 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,5
d30The DISTANCE action with label d30 calculates the following quantities: Quantity    Type    Description  
d30 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,26
d31The DISTANCE action with label d31 calculates the following quantities: Quantity    Type    Description  
d31 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,47
d32The DISTANCE action with label d32 calculates the following quantities: Quantity    Type    Description  
d32 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,61
d33The DISTANCE action with label d33 calculates the following quantities: Quantity    Type    Description  
d33 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,73
d34The DISTANCE action with label d34 calculates the following quantities: Quantity    Type    Description  
d34 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,88
d35The DISTANCE action with label d35 calculates the following quantities: Quantity    Type    Description  
d35 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,102
d36The DISTANCE action with label d36 calculates the following quantities: Quantity    Type    Description  
d36 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,109
d37The DISTANCE action with label d37 calculates the following quantities: Quantity    Type    Description  
d37 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,5
d38The DISTANCE action with label d38 calculates the following quantities: Quantity    Type    Description  
d38 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,26
d39The DISTANCE action with label d39 calculates the following quantities: Quantity    Type    Description  
d39 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,47
d40The DISTANCE action with label d40 calculates the following quantities: Quantity    Type    Description  
d40 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,61
d41The DISTANCE action with label d41 calculates the following quantities: Quantity    Type    Description  
d41 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,73
d42The DISTANCE action with label d42 calculates the following quantities: Quantity    Type    Description  
d42 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,88
d43The DISTANCE action with label d43 calculates the following quantities: Quantity    Type    Description  
d43 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,102
d44The DISTANCE action with label d44 calculates the following quantities: Quantity    Type    Description  
d44 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,109
d45The DISTANCE action with label d45 calculates the following quantities: Quantity    Type    Description  
d45 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,123

#Deep-TDA CV
deepTDAThe PYTORCH_MODEL action with label deepTDA calculates the following quantities: Quantity    Type    Description  
deepTDA.node-0 scalar Model outputs  This is the 0th of these quantities: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=chignolin_deepTDA.pt ARGthe labels of the values from which the function is calculated=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16,d17,d18,d19,d20,d21,d22,d23,d24,d25,d26,d27,d28,d29,d30,d31,d32,d33,d34,d35,d36,d37,d38,d39,d40,d41,d42,d43,d44,d45

#Surrogate Model (Deep-TDA)
lasso_TDAThe COMBINE action with label lasso_TDA calculates the following quantities: Quantity    Type    Description  
lasso_TDA scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d7,d11,d16,d19,d23,d30,d33,d37, COEFFICIENTS the coefficients of the arguments in your function=-0.7286,-1.1949,-1.7543,1.4975,1.1449,4.3191,-1.6496,1.8272, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
 
lassoCV_TDAThe MATHEVAL action with label lassoCV_TDA calculates the following quantities: Quantity    Type    Description  
lassoCV_TDA scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=lasso_TDA FUNCthe function you wish to evaluate=x-3.2078 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

#Deep-TICA CV
deepTICAThe PYTORCH_MODEL action with label deepTICA calculates the following quantities: Quantity    Type    Description  
deepTICA.node-0 scalar Model outputs  This is the 0th of these quantities
deepTICA.node-1 scalar Model outputs  This is the 1th of these quantities: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=chignolin3_deeptica.pt ARGthe labels of the values from which the function is calculated=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16,d17,d18,d19,d20,d21,d22,d23,d24,d25,d26,d27,d28,d29,d30,d31,d32,d33,d34,d35,d36,d37,d38,d39,d40,d41,d42,d43,d44,d45

#Surrogate Model (Deep-TICA)
lasso_TICAThe COMBINE action with label lasso_TICA calculates the following quantities: Quantity    Type    Description  
lasso_TICA scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d5,d12,d13,d14,d16,d17,d19,d22,d24,d27,d30,d31,d32,d33,d34,d37,d38,d39,d42,d43, COEFFICIENTS the coefficients of the arguments in your function=-0.6432,0.8959,-1.4165,0.9420,0.3441,-0.1968,-0.9315,0.2640,-0.0790,-1.0431,-0.9526,0.1253,0.5120,0.3345,0.5238,-0.6802,0.4996,-0.0392,-0.1279,0.0068, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

lassoCV_TICAThe MATHEVAL action with label lassoCV_TICA calculates the following quantities: Quantity    Type    Description  
lassoCV_TICA scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=lasso_TICA FUNCthe function you wish to evaluate=x+0.6402 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

#OPES Simulation
opesThe OPES_METAD action with label opes calculates the following quantities: Quantity    Type    Description  
opes.bias scalar the instantaneous value of the bias potential
opes.rct scalar estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opes.zed scalar estimate of Z_n. should become flat once no new CV-space region is explored
opes.neff scalar effective sample size
opes.nker scalar total number of compressed kernels used to represent the bias: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
  ARGthe labels of the scalars on which the bias will act=deepTDA.node-0
  #ARG=lassoCV_TDA
  #ARG=deepTICA.node-0
  #ARG=lassoCV_TICA 
  PACEthe frequency for kernel deposition=500
  TEMP temperature=340
  BARRIERthe free energy barrier to be overcome=30
... 
opes: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ...
  ARGthe labels of the scalars on which the bias will act=deepTDA.node-0
  #ARG=lassoCV_TDA
  #ARG=deepTICA.node-0
  #ARG=lassoCV_TICA 
  PACEthe frequency for kernel deposition=500
  TEMP temperature=340
  BARRIERthe free energy barrier to be overcome=30
 SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1 FILE a file in which the list of all deposited kernels is stored=KERNELS
... 

# PRINT
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=deepTDA.node-0,lassoCV_TDA,deepTICA.node-0,lassoCV_TICA,opes.* FILEthe name of the file on which to output these quantities=COLVAR
Quantity	Type	Description
PROTEIN	atoms	indices of atoms specified in GROUP
PLUMED-NEST

The public repository of the PLUMED consortium
